DNA-metabarcoding analyses of the grapevine wood fungal community in the Krasnodar Region and Crimea
- Authors: Blinova S.A.1,2, Shvartsev A.A.2, Alekseev Y.I.2,3, Stranishevskaya E.P.3, Ilnitskaya E.T.4, Makarkina M.V.4, Soloviev A.A.1
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Affiliations:
- All-Russia Research Institute of Agricultural Biotechnology
- LLC “Syntol”
- National Research Institute for Grape and Wine Magarach Russian Academy of Sciences
- North Caucasus Federal Scientific Center for Horticulture, Viticulture, Winemaking
- Issue: Vol 20, No 2 (2022)
- Pages: 89-100
- Section: Genetic basis of ecosystems evolution
- URL: https://journals.rcsi.science/ecolgenet/article/view/106312
- DOI: https://doi.org/10.17816/ecogen106312
- ID: 106312
Cite item
Abstract
Grapes are an economically important agricultural plant. Studies of the Grapevine microbiota and rhizosphere have become increasingly important in the last decade. The importance of such research is also supported by the fact that grapes are a perennial, long-used crop.
In this work, we present the results of a DNA-metabarcoding analysis of the fungal community of grape wood, collected from vineyards in the Krasnodar Territory and the Southern Coast of Crimea, and considered approaches to the analysis of DNA-metabarcoding data. Classifier is Naïve base (“sklearn”) based on machine learning is more informative metagenomic data classifier than BLAST+ (local alignment) and Vsearch (global alignment). Analysis of the ITS locus revealed the largest number of taxa, which was confirmed for all types of classifiers used in the study. Primers for the ITS locus showed a high specificity of fungal DNA in comparison with the LSU and SSU loci. The most common genera in the fungal community are Acidea, Alternaria, Cladosporium and Fusarium. Significant differences were revealed in the assessment of alpha and beta diversity in the analysis of samples from different regions. This article presents an analysis of the wood grapevine fungal community and ways to ASV classification. This study is the first to describe the endophytic fungal communities of the Krasnodar Territory and the Crimea vines using the analysis of DNA metabarcoding data.
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##article.viewOnOriginalSite##About the authors
Sofiia A. Blinova
All-Russia Research Institute of Agricultural Biotechnology; LLC “Syntol”
Author for correspondence.
Email: sofya.blinova@yandex.ru
ORCID iD: 0000-0001-6782-8353
SPIN-code: 9148-3765
Scopus Author ID: 57217069755
Postgraduate Student, Junior Researcher
Russian Federation, Moscow; MoscowAleksey A. Shvartsev
LLC “Syntol”
Email: alexey.sva@yandex.ru
ORCID iD: 0000-0002-2786-9860
SPIN-code: 9792-6398
Researcher
Russian Federation, MoscowYakov I. Alekseev
LLC “Syntol”; National Research Institute for Grape and Wine Magarach Russian Academy of Sciences
Email: jalex01@mail.ru
ORCID iD: 0000-0002-1696-7684
SPIN-code: 8145-5586
Cand. Sci. (Biol.), Director of Science
Russian Federation, Moscow; YaltaElena P. Stranishevskaya
National Research Institute for Grape and Wine Magarach Russian Academy of Sciences
Email: stranishevskayaelena@gmail.com
ORCID iD: 0000-0002-2840-5638
Scopus Author ID: 57190218360
Dr. Sci. (Agricult.), Professor
Russian Federation, YaltaElena T. Ilnitskaya
North Caucasus Federal Scientific Center for Horticulture, Viticulture, Winemaking
Email: ilnitskaya79@mail.ru
ORCID iD: 0000-0002-2446-0971
SPIN-code: 7075-1328
Scopus Author ID: 57192072976
Cand. Sci. (Biol.), Head of Laboratory
Russian Federation, KrasnodarMarina V. Makarkina
North Caucasus Federal Scientific Center for Horticulture, Viticulture, Winemaking
Email: konec_citatu@mail.ru
ORCID iD: 0000-0002-3397-0666
SPIN-code: 3833-1636
Scopus Author ID: 57204108200
Junior Researcher
Russian Federation, KrasnodarAlexander A. Soloviev
All-Russia Research Institute of Agricultural Biotechnology
Email: a.soloviev70@gmail.com
ORCID iD: 0000-0003-4480-8776
SPIN-code: 3431-5168
Scopus Author ID: 35732425900
Dr. Sci. (Biol.), Professor RAS, Head of Laboratory
Russian Federation, MoscowReferences
- Jayawardena RS, Purahong W, Zhang W, et al. Biodiversity of fungi on Vitis vinifera L. revealed by traditional and high-resolution culture-independent approaches. Fungal Divers. 2018;90:1–84. doi: 10.1007/s13225-018-0398-4
- Fuchs M. Grapevine viruses: a multitude of diverse species with simple but overall poorly adopted management solutions in the vineyard. J Plant Pathol. 2020;102(3):643–653. doi: 10.1007/s42161-020-00579-2
- Salvetti E, Campanaro S, Campedelli I, et al. Whole-Metagenome-Sequencing-Based Community Profiles of Vitis vinifera L. cv. Corvina Berries Withered in Two Post-harvest Conditions. Front Microbiol. 2016;7:937. doi: 10.3389/fmicb.2016.00937
- Mori N, Quaglino F, Tessari F, et al. Investigation on ‘bois noir’ epidemiology in north-eastern Italian vineyards through a multidisciplinary approach. Ann Appl Biol. 2014;166(1):75–89. doi: 10.1111/aab.12165
- Burovinskaya MV, Yurchenko EG. Tracheomycosis grape diseases and measures of their restrictions. Fruit growing and viticulture of South Russia. 2020;(63):270–284. (In Russ.) doi: 10.30679/2219-5335-2020-3-63-270-284
- Savchuk NV, Yurchenko EG, Vinogradova SV, Porotikova EV. Causative agents of Fusarium wilt of the reproductive organs of grapes. Ways of infection. Proceedings of the V International science and practice conferences: “Sovremennoe sostoyanie, problemy i perspektivy razvitiya agrarnoi nauki”; 2020 Sept 21–25. P. 95–97. (In Russ.) doi: 10.33952/2542-0720-2020-5-9-10-45
- Blackwell M. The Fungi: 1, 2, 3 … 5.1 million species? Am J Bot. 2011;98(3):426–438. doi: 10.3732/ajb.1000298
- Berlanas C, Berbegal M, Elena G, et al. The Fungal and Bacterial Rhizosphere Microbiome Associated With Grapevine Rootstock Genotypes in Mature and Young Vineyards. Front Microbiol. 2019;10:1142. doi: 10.3389/fmicb.2019.01142
- Úrbez-Torres JR, Gubler WD. Susceptibility of grapevine pruning wounds to infection by Lasiodiplodia theobromae and Neofusicoccum parvum. Plant Pathol. 2010;60(2):261–270. doi: 10.1111/j.1365-3059.2010.02381.x
- Jayawardena R, Purahong W, Zhang W, et al. Biodiversity of fungi on Vitis vinifera L. revealed by traditional and high-resolution culture-independent approaches. Fungal Divers. 2018;90(1):1–84. doi: 10.1007/s13225-018-0398-4
- Lade SB, Štraus D, Oliva J. Variation in Fungal Community in Grapevine (Vitis vinifera) Nursery Stock Depends on Nursery, Variety and Rootstock. Journal of Fungi. 2022;8(1):47. doi: 10.3390/jof8010047
- Mendes R, Kruijt M, De Bruijn I, et al. Deciphering the Rhizosphere Microbiome for Disease-Suppressive Bacteria. Science. 2011;3329(6033):1097–1100. doi: 10.1126/science.1203980
- Janssen PH. Identifying the Dominant Soil Bacterial Taxa in Libraries of 16S rRNA and 16S rRNA Genes. Appl Environ Microbiol. 2006;72(3):1719–1728. doi: 10.1128/aem.72.3.1719-1728.2006
- Buffet-Bataillon S, Rizk G, Cattoir V, et al. Efficient and Quality-Optimized Metagenomic Pipeline Designed for Taxonomic Classification in Routine Microbiological Clinical Tests. Microorganisms. 2022;10(4):711. doi: 10.3390/microorganisms10040711
- Zarraonaindia I, Owens SM, Weisenhorn P, et al. The Soil Microbiome Influences Grapevine-Associated Microbiota. mBio. 2015;6(2): e02527–14. doi: 10.1128/mbio.02527-14
- Niem JM, Billones-Baaijens R, Stodart B, Savocchia S. Diversity Profiling of Grapevine Microbial Endosphere and Antagonistic Potential of Endophytic Pseudomonas Against Grapevine Trunk Diseases. Front Microbiol. 2020;11:477. doi: 10.3389/fmicb.2020.00477
- Schoch CL, Seifert KA, Huhndorf S, et al. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. PNAS. 2012;109(16):6241–6246. doi: 10.1073/pnas.1117018109
- Ishii N, Ishida S, Kagami M. PCR primers for assessing community structure of aquatic fungi including Chytridiomycota and Cryptomycota. Fungal Ecol. 2015;13:33–43. doi: 10.1016/j.funeco.2014.08.004
- Jones EBG, Devadatha B, Abdel-Wahab MA, et al. Phylogeny of new marine Dothideomycetes and Sordariomycetes from mangroves and deep-sea sediments. Botanica Marina. 2020;63(2):155–181. doi: 10.1515/bot-2019-0014
- Tedersoo L, Anslan S, Bahram M, et al. Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi. MycoKeys. 2015;10:1–43. doi: 10.3897/mycokeys.10.4852
- Bioinformatics.babraham.ac.uk [Internet]. Babraham Bioinformatics [cited: 2021 Dec 11]. Available from: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
- Multiqc.info [Internet]. MultiQC [cited: 2021 Dec 11]. Available from: https://www.multiqc.info/
- Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–2120. doi: 10.1093/bioinformatics/btu170
- Bolyen E, Rideout JR, Dillon MR, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME2. Nat Biotechnol. 2019;37(8):852–857. doi: 10.1038/s41587-019-0209-9
- Callahan BJ, McMurdie PJ, Rosen MJ, et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13(7):581–583. doi: 10.1038/nmeth.3869
- Camacho C, Coulouris G, Avagyan V, et al. BLAST+: architecture and applications. BMC Bioinformatics. 2009;10(1):421. doi: 10.1186/1471-2105-10-421
- Rognes T, Flouri T, Nichols B, et al. VSEARCH: a versatile open source tool for metagenomics. PeerJ. 2016;4: e2584. doi: 10.7717/peerj.2584
- Pedregosa F, Varoquaux G, Gramfort A, et al. Scikit-learn: Machine Learning in Python. J Mach Learn Res. 2012;12:2825–2830. doi: 10.48550/arXiv.1201.0490
- Nilsson RH, Larsson K-H, Taylor AFS, et al. The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. Nucleic Acids Res. 2018;47(D1): D259–D264. doi: 10.1093/nar/gky1022
- Robeson MS II, O’Rourke DR, Kaehler BD, et al. RESCRIPt: Reproducible sequence taxonomy reference database management for the masses. bioRxiv. 2020: ID326504. doi: 10.1101/2020.10.05.326504
- McMurdie PJ, Holmes S. phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data. PLoS One. 2013;8(4): e61217. doi: 10.1371/journal.pone.0061217
- Wickham H. ggplot2: Elegant Graphics for Data Analysis. In: Gentleman R, Hornik K, Parmigiani G, editors. Use R! New York: Springer-Verlag, 2016. P. 189–201. doi: 10.1007/978-3-319-24277-4_9
- González V, Tello ML. The endophytic mycota associated with Vitis vinifera in central Spain. Fungal Divers. 2010;47(1):29–42. doi: 10.1007/s13225-010-0073-x
- Aćimović SG, Harmon CL, Bec S, et al. First Report of Diplodia corticola Causing Decline of Red Oak (Quercus rubra) Trees in Maine. Plant Dis. 2016;100(3):649. doi: 10.1094/pdis-09-15-0994-pdn
- Phillips AJL, Alves A, Abdollahzadeh J, et al. The Botryosphaeriaceae: genera and species known from culture. Stud Mycol. 2013;76(1):51–167. doi: 10.3114/sim0021